Transform PSSM (Position-Specific Scoring Matrix) to a KMER

This function transforms a PSSM into a k-mer of a given length.

Usage

pssm_to_kmer(pssm, kmer_length = NULL, pos_bits_thresh = NULL, prior = 0.01)

pssm: PSSM matrix or data frame. The PSSM must have at least kmer_length rows.
kmer_length: The length of the k-mer to return. If NULL - the length of the k-mer is equal to the number of rows in the PSSM.
pos_bits_thresh: A numeric value indicating the minimum number of bits per position to include the nucleotide in the k-mer. If the nucleotide does not meet this threshold, it is replaced with 'N'. Default is NULL.
prior: A numeric value indicating the prior probability for each nucleotide. Default is 0.01.

A character vector of length 1 containing the k-mer.

pssm_to_kmer(get_motif_pssm("HOMER.AP_1"))
#> [1] "ATGACTCATC"
plot_pssm_logo_dataset("HOMER.AP_1")